Hi,
I would recommend temporarily switching to the default template of Joomla to see if you have the same issue with the pagination.
If yes, then we'll need a backend and a FTP access in order to check on the situation.
If no, then its either coming from the pagination.php file of the template, as you guessed, or a view override file under the templates/YOU_TEMPLATE/html/com_hikashop/product/ folder. So you can check if you have this folder, and if so, you can try renaming it via FTP to disable all the overrides for the product pages, including the listing. That way, you can check if you still have the issue, which could confirm or not that the issue comes from one of the files in there.